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SkullStripper.cxx
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SkullStripper.cxx
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#if defined(_MSC_VER)
#pragma warning ( disable : 4786 )
#endif
#include "stdlib.h"
#include "stdio.h"
#include "math.h"
#include "set"
#include "itkPoint.h"
#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageSeriesReader.h"
#include "itkImageFileWriter.h"
#include "itkImageRegionIteratorWithIndex.h"
#include "itkGDCMImageIO.h"
#include "itkGDCMSeriesFileNames.h"
#include "itkNearestNeighborInterpolateImageFunction.h"
#include "itkLinearInterpolateImageFunction.h"
#include "itkSignedMaurerDistanceMapImageFilter.h"
#include "itkSphereSpatialFunction.h"
#include "itkFloodFilledSpatialFunctionConditionalIterator.h"
#include "itkFloodFilledImageFunctionConditionalIterator.h"
#include "itkVotingBinaryIterativeHoleFillingImageFilter.h"
#include "itkBinaryThresholdImageFunction.h"
#include "itkBinaryDilateImageFilter.h"
#include "itkBinaryErodeImageFilter.h"
#include "itkExtractImageFilter.h"
#include "itkLinearInterpolateImageFunction.h"
#include "itkScalarImageToHistogramGenerator.h"
#include "itkFuzzyClassificationImageFilter.h"
#include "itkCastImageFilter.h"
#include "itkBinaryThresholdImageFilter.h"
#include "itkConnectedComponentImageFilter.h"
#include "itkRelabelComponentImageFilter.h"
#include "itkBinaryBallStructuringElement.h"
#include "itkGrayscaleMorphologicalClosingImageFilter.h"
#include "itkGrayscaleMorphologicalOpeningImageFilter.h"
#include "itkGrayscaleFunctionErodeImageFilter.h"
#include "vtkSmartPointer.h"
#include "vtkIdList.h"
#include "vtkPolyData.h"
#include "vtkXMLPolyDataWriter.h"
#include "vtkPolyDataPointSampler.h"
#include "SkullStripperCLP.h"
static const float PI = 3.1415926535897932;
#define X .525731112119133606
#define Z .850650808352039932
#ifndef M_PI
#define M_PI 3.1415926535897932
#endif
#ifndef M_PI_2
#define M_PI_2 1.5707963267948966
#endif
//Vertices, triangles, edges of a single icosahedron
static double vert[12][3] = {
{-X, 0.0, Z}, {X, 0.0, Z}, {-X, 0.0, -Z}, {X, 0.0, -Z},
{0.0, Z, X}, {0.0, Z, -X}, {0.0, -Z, X}, {0.0, -Z, -X},
{Z, X, 0.0}, {-Z, X, 0.0}, {Z, -X, 0.0}, {-Z, -X, 0.0}
};
static int triang[20][3] = {
{0,4,1}, {0,9,4}, {9,5,4}, {4,5,8}, {4,8,1},
{8,10,1}, {8,3,10}, {5,3,8}, {5,2,3}, {2,7,3},
{7,10,3}, {7,6,10}, {7,11,6}, {11,0,6}, {0,1,6},
{6,1,10}, {9,0,11}, {9,11,2}, {9,2,5}, {7,2,11}
};
static int edge[30][2] = {
{0,1}, {0,4}, {0,6}, {0,9}, {0,11}, {1,4}, {1,6}, {1,8}, {1,10}, {2,3},
{2,5}, {2,7}, {2,9}, {2,11}, {3,5}, {3,7}, {3,8}, {3,10}, {4,5}, {4,8},
{4,9}, {5,8}, {5,9}, {6,7}, {6,10}, {6,11}, {7,10}, {7,11}, {8,10}, {9,11}
};
itk::Point<float, 3> COG;
typedef std::vector<vtkIdType> NeighborhoodType;
const unsigned int ImageDimension = 3;
typedef signed short PixelType;
typedef itk::Image< PixelType, ImageDimension > ImageType;
typedef itk::Image<unsigned char, ImageDimension> LabelImageType;
typedef itk::Image<double, ImageDimension> FloatImageType;
typedef itk::ImageFileReader< ImageType > ImageReaderType;
typedef float HistogramMeasurementType;
typedef itk::Statistics::ScalarImageToHistogramGenerator< ImageType > GeneratorType;
typedef GeneratorType::HistogramType HistogramType;
LabelImageType::Pointer BinaryErodeFilter3D ( LabelImageType::Pointer & img , unsigned int ballsize )
{
typedef itk::BinaryBallStructuringElement<unsigned char, 3> KernalType;
typedef itk::BinaryErodeImageFilter<LabelImageType, LabelImageType, KernalType> ErodeFilterType;
ErodeFilterType::Pointer erodeFilter = ErodeFilterType::New();
erodeFilter->SetInput( img );
KernalType ball;
KernalType::SizeType ballSize;
for (int k = 0; k < 3; k++)
{
ballSize[k] = ballsize;
}
ball.SetRadius(ballSize);
ball.CreateStructuringElement();
erodeFilter->SetKernel( ball );
erodeFilter->Update();
return erodeFilter->GetOutput();
}
LabelImageType::Pointer BinaryDilateFilter3D ( LabelImageType::Pointer & img , unsigned int ballsize )
{
typedef itk::BinaryBallStructuringElement<unsigned char, 3> KernalType;
typedef itk::BinaryDilateImageFilter<LabelImageType, LabelImageType, KernalType> DilateFilterType;
DilateFilterType::Pointer dilateFilter = DilateFilterType::New();
dilateFilter->SetInput( img );
KernalType ball;
KernalType::SizeType ballSize;
for (int k = 0; k < 3; k++)
{
ballSize[k] = ballsize;
}
ball.SetRadius(ballSize);
ball.CreateStructuringElement();
dilateFilter->SetKernel( ball );
dilateFilter->Update();
return dilateFilter->GetOutput();
}
LabelImageType::Pointer BinaryOpeningFilter3D ( LabelImageType::Pointer & img , unsigned int ballsize )
{
LabelImageType::Pointer imgErode = BinaryErodeFilter3D( img, ballsize );
return BinaryDilateFilter3D( imgErode, ballsize );
}
LabelImageType::Pointer BinaryClosingFilter3D ( LabelImageType::Pointer & img , unsigned int ballsize )
{
LabelImageType::Pointer imgDilate = BinaryDilateFilter3D( img, ballsize );
return BinaryErodeFilter3D( imgDilate, ballsize );
}
void PolyDataToLabelMap( vtkPolyData* polyData, LabelImageType::Pointer label)
{
vtkSmartPointer<vtkPolyDataPointSampler> sampler = vtkSmartPointer<vtkPolyDataPointSampler>::New();
sampler->SetInputData( polyData );
sampler->SetDistance( 0.75 );
sampler->GenerateEdgePointsOn();
sampler->GenerateInteriorPointsOn();
sampler->GenerateVertexPointsOn();
sampler->Update();
std::cout << polyData->GetNumberOfPoints() << std::endl;
std::cout << sampler->GetOutput()->GetNumberOfPoints() << std::endl;
label->FillBuffer( 0 );
for (int k = 0; k < sampler->GetOutput()->GetNumberOfPoints(); k++)
{
double *pt = sampler->GetOutput()->GetPoint( k );
LabelImageType::PointType pitk;
pitk[0] = pt[0];
pitk[1] = pt[1];
pitk[2] = pt[2];
LabelImageType::IndexType idx;
label->TransformPhysicalPointToIndex( pitk, idx );
if ( label->GetLargestPossibleRegion().IsInside(idx) )
{
label->SetPixel( idx, 1 );
}
}
// do morphological closing
int ballSize = 2;
LabelImageType::Pointer closedLabel = BinaryClosingFilter3D( label, ballSize );
//LabelImageType::Pointer closedLabel = BinaryDilateFilter3D( label2, 2 );
itk::ImageRegionIteratorWithIndex<LabelImageType>
itLabel (closedLabel, closedLabel->GetLargestPossibleRegion() );
// do flood fill using binary threshold image function
typedef itk::BinaryThresholdImageFunction<LabelImageType> ImageFunctionType;
ImageFunctionType::Pointer func = ImageFunctionType::New();
func->SetInputImage( closedLabel );
func->ThresholdBelow(0);
FloatImageType::IndexType idx;
label->TransformPhysicalPointToIndex( COG, idx );
itk::FloodFilledImageFunctionConditionalIterator<LabelImageType, ImageFunctionType>
floodFill( closedLabel, func, idx );
for (floodFill.GoToBegin(); !floodFill.IsAtEnd(); ++floodFill)
{
LabelImageType::IndexType i = floodFill.GetIndex();
closedLabel->SetPixel( i, 1 );
}
LabelImageType::Pointer finalLabel = BinaryClosingFilter3D( closedLabel, ballSize );
for (itLabel.GoToBegin(); !itLabel.IsAtEnd(); ++itLabel)
{
LabelImageType::IndexType i = itLabel.GetIndex();
label->SetPixel( i, finalLabel->GetPixel(i) );
}
return;
}
int FindTopSlice( ImageType::Pointer fixed )
{
ImageType::SpacingType spacing = fixed->GetSpacing();
ImageType::RegionType region = fixed->GetLargestPossibleRegion();
ImageType::SizeType size = region.GetSize();
std::vector<double> projection( size[2] );
std::vector<double> nVoxels( size[2] );
for (::size_t k = 0; k < size[2]; k++)
{
projection[k] = 0;
nVoxels[k] = 0;
}
ImageType::RegionType centerRegion = fixed->GetLargestPossibleRegion();
for (int k = 0; k < 3; k++)
{
centerRegion.SetIndex( k, centerRegion.GetIndex(k)+centerRegion.GetSize(k)/2-5 );
centerRegion.SetSize( k, 11 );
}
itk::ImageRegionIteratorWithIndex<ImageType> itc( fixed, centerRegion );
double aveIntensity = 0;
for ( itc.GoToBegin(); !itc.IsAtEnd(); ++itc )
{
aveIntensity += static_cast<double>( itc.Get() );
}
aveIntensity /= (11.0*11.0*11.0);
// find the right slice
itk::ImageRegionIteratorWithIndex<ImageType> it( fixed, region );
for (it.GoToBegin(); !it.IsAtEnd(); ++it)
{
ImageType::IndexType idx = it.GetIndex();
double p = static_cast<double> (it.Get());
if( p >= aveIntensity/10 )
{
projection[idx[2]] += p;
nVoxels[idx[2]] += 1;
}
}
for (ImageType::SizeType::SizeValueType k = 0; k < size[2]; k++)
{
projection[k] /= nVoxels[k];
}
double noiselevel = 0;
double noiseslice = 0;
unsigned int topslice=size[2]-1;
for (long k = size[2]-1; k >=0; k--)
{
if (projection[k] == 0)
{
continue;
}
else if(noiselevel == 0)
{
noiselevel = projection[k];
noiseslice = 1;
}
else
{
if (projection[k] > noiselevel*2 || projection[k] > aveIntensity/3.0)
{
topslice = k;
break;
}
else
{
noiselevel = ((noiselevel*noiseslice)+projection[k])/(noiseslice+1);
noiseslice ++;
}
}
}
unsigned short signalThreshold = static_cast<unsigned short>(static_cast<double>(projection[topslice])/2);
//for (int k = 0; k < size[2]; k++)
//{
//std::cout << k << " " << projection[k] << "; \n";
//}
//std::cout << std::endl;
std::cout << "Signal level: " << signalThreshold << std::endl;
std::cout << "Top of head at slice " << topslice << std::endl;
return topslice;
}
ImageType::PixelType FindWhiteMatterPeak ( HistogramType::Pointer histogram )
{
HistogramType::SizeType size = histogram->GetSize();
std::cout << "Histogram size: " << size << std::endl;
PixelType t95 = static_cast<PixelType> (histogram->Quantile(0, 0.95));
std::cout << "t95 = " << t95 << " Histogram bins: " << size[0] << std::endl;
std::vector<ImageType::PixelType> intensity( size[0] );
std::vector<float> frequency( size[0] );
for (unsigned int k = 0; k < size[0]; k++)
{
intensity[k] = histogram -> GetBinMin( 0, k );
frequency[k] = histogram->GetFrequency ( k );
}
// suppress the backgroud values
frequency[0] = 0;
frequency[1] = 0;
// do simple five point average
std::vector<unsigned int> smoothedfrequency( size[0] );
for (unsigned int k = 2; k < size[0]-2; k++)
{
double d = 0;
for (int m = -2; m <=2; m++)
{
d += static_cast<double> (frequency[k+m]);
}
smoothedfrequency[k] = static_cast<unsigned int> ( d/5 );
}
return t95;
}
void ComputeVertexNeighbors(vtkIdType iVertexId, vtkPolyData* pMesh, std::vector<vtkIdType>& pIdRet)
{
std::set<vtkIdType> setNeighbors;
vtkIdType* pIncidentCells;
vtkIdType iNumCells;
pMesh->GetPointCells(iVertexId, iNumCells, pIncidentCells);
int j;
const vtkIdType* pIncidentPoints;
vtkIdType iNumPoints;
for(int i=0; i<iNumCells; ++i)
{
pMesh->GetCellPoints(pIncidentCells[i], iNumPoints, pIncidentPoints);
for(j=0; j<iNumPoints; ++j)
if(pIncidentPoints[j]!=iVertexId)
setNeighbors.insert(pIncidentPoints[j]);
}
// make pointIds in order
std::vector<vtkIdType> pIds;
for (std::set<vtkIdType>::iterator m = setNeighbors.begin(); m != setNeighbors.end(); m++)
{
pIds.push_back( *m );
}
// find first edge
vtkIdType Id0 = pIds[0];
vtkIdType Id1 = 0;
for (::size_t k = 1; k < pIds.size(); k++)
{
if ( !pMesh->IsEdge( Id0, pIds[k]) )
{
continue;
}
Id1 = pIds[k];
break;
}
// figure out if Id0 and Id1 is in the right order;
double pc[3];
memcpy( pc, pMesh->GetPoint(iVertexId), 3*sizeof(double) );
double p0[3];
memcpy( p0, pMesh->GetPoint(Id0), 3*sizeof(double) );
double p1[3];
memcpy( p1, pMesh->GetPoint(Id1), 3*sizeof(double) );
for (int m = 0; m <3; m++)
{
p0[m] -= pc[m];
p1[m] -= pc[m];
}
double op[3];
op[0] = p0[1]*p1[2]-p0[2]*p1[1];
op[1] = p0[2]*p1[0]-p0[0]*p1[2];
op[2] = p0[0]*p1[1]-p0[1]*p1[0];
double ip = op[0]*pc[0]+op[1]*pc[1]+op[2]*pc[2];
if (ip < 0) // swap Id0 and Id1;
{
vtkIdType tempId = Id0;
Id0 = Id1;
Id1 = tempId;
}
pIdRet.push_back( Id0 );
pIdRet.push_back( Id1 );
for (::size_t k = 2; k < pIds.size(); k++)
{
vtkIdType curentId = pIdRet[k-1];
for (::size_t m = 0; m < pIds.size(); m++)
{
vtkIdType tempId = pIds[m];
int InSet = 0;
for (::size_t n = 0; n < pIdRet.size(); n++)
{
if (pIdRet[n] == tempId)
{
InSet = 1;
break;
}
}
if (InSet == 1)
{
continue;
}
if ( pMesh->IsEdge(curentId, tempId) )
{
pIdRet.push_back( tempId );
break;
}
}
}
}
vtkPolyData* TessellateIcosahedron(int level)
{
//Calculate n_vertex, n_triag
int n=0;
if(level > 2)
{
for(int i=1; i<(level-1); i++)
n += i;
}
int n_vert = 12 + (level - 1)*30 + n*20;
int numtriags = 0;
if(level == 1)
{
numtriags = 20;
}
else
{
n = 1;
do
{
for(int m=1; m<=n; m++)
{
numtriags = numtriags + 3;
if(m != n)
numtriags = numtriags + 3;
}
n++;
}while(n<=level);
numtriags = numtriags * 20;
numtriags = numtriags / 3;
}
typedef double Point3[3];
//Allocate datas
Point3* all_vert = new Point3[n_vert];
Point3* all_triangs = new Point3[numtriags*3];//all possible vertices in triangs
int * triangs = new int[3*numtriags];
int i, m, k;
double x1, x2, y1, y2, z1, z2, x3, y3, z3;
double dx12, dy12, dz12, dx23, dy23, dz23;
double length;
double epsilon = 0.00001;//machine epsilon??
memcpy(all_vert, vert, 12*sizeof(Point3));
//std::cout<<"after memcpy"<<std::endl;
k=12;
for(i=0; i<30; i++)
{
x1 = vert[edge[i][0] ][0];
y1 = vert[edge[i][0] ][1];
z1 = vert[edge[i][0] ][2];
x2 = vert[edge[i][1] ][0];
y2 = vert[edge[i][1] ][1];
z2 = vert[edge[i][1] ][2];
dx12 = (x2 - x1)/level;
dy12 = (y2 - y1)/level;
dz12 = (z2 - z1)/level;
for(n=1; n<level; n++)
{
all_vert[k][0] = x1 + n*dx12;
all_vert[k][1] = y1 + n*dy12;
all_vert[k][2] = z1 + n*dz12;
length = sqrt(static_cast<double> (all_vert[k][0]*all_vert[k][0]+
all_vert[k][1]*all_vert[k][1]+
all_vert[k][2]*all_vert[k][2]));
all_vert[k][0] /= length;
all_vert[k][1] /= length;
all_vert[k][2] /= length;
k++;
}
}
if(level > 2)
{
for(i=0; i<20; i++)
{
x1 = vert[triang[i][0] ][0];
y1 = vert[triang[i][0] ][1];
z1 = vert[triang[i][0] ][2];
x2 = vert[triang[i][1] ][0];
y2 = vert[triang[i][1] ][1];
z2 = vert[triang[i][1] ][2];
x3 = vert[triang[i][2] ][0];
y3 = vert[triang[i][2] ][1];
z3 = vert[triang[i][2] ][2];
dx12 = (x2 - x1)/level;
dy12 = (y2 - y1)/level;
dz12 = (z2 - z1)/level;
dx23 = (x3 - x2)/level;
dy23 = (y3 - y2)/level;
dz23 = (z3 - z2)/level;
n = 1;
do
{
for(m=1; m<=n; m++)
{
all_vert[k][0] = x1 + (n+1)*dx12 + m*dx23;
all_vert[k][1] = y1 + (n+1)*dy12 + m*dy23;
all_vert[k][2] = z1 + (n+1)*dz12 + m*dz23;
length = sqrt((double) all_vert[k][0]*all_vert[k][0]+
all_vert[k][1]*all_vert[k][1]+
all_vert[k][2]*all_vert[k][2]);
all_vert[k][0] /= length;
all_vert[k][1] /= length;
all_vert[k][2] /= length;
k++;
}
n++;
}while( n<=(level-2) );
}
}
numtriags=0;
//std::cout<<"before get triangulation"<<std::endl;
//std::cout<<n_triangs<<std::endl;
// get triangulation
if (level > 1)
{
for(i=0; i<20; i++)
{
x1 = vert[triang[i][0] ][0];
y1 = vert[triang[i][0] ][1];
z1 = vert[triang[i][0] ][2];
x2 = vert[triang[i][1] ][0];
y2 = vert[triang[i][1] ][1];
z2 = vert[triang[i][1] ][2];
x3 = vert[triang[i][2] ][0];
y3 = vert[triang[i][2] ][1];
z3 = vert[triang[i][2] ][2];
dx12 = (x2 - x1)/level;
dy12 = (y2 - y1)/level;
dz12 = (z2 - z1)/level;
dx23 = (x3 - x2)/level;
dy23 = (y3 - y2)/level;
dz23 = (z3 - z2)/level;
n = 1;
do
{
for(m=1; m<=n; m++)
{
// Draw lower triangle
all_triangs[numtriags][0] = x1 + n*dx12 + m*dx23;
all_triangs[numtriags][1] = y1 + n*dy12 + m*dy23;
all_triangs[numtriags][2] = z1 + n*dz12 + m*dz23;
length = sqrt((double) all_triangs[numtriags][0]*all_triangs[numtriags][0]+
all_triangs[numtriags][1]*all_triangs[numtriags][1]+
all_triangs[numtriags][2]*all_triangs[numtriags][2]);
all_triangs[numtriags][0] /= length;
all_triangs[numtriags][1] /= length;
all_triangs[numtriags][2] /= length;
numtriags++;
all_triangs[numtriags][0] = x1 + (n-1)*dx12 + (m-1)*dx23;
all_triangs[numtriags][1] = y1 + (n-1)*dy12 + (m-1)*dy23;
all_triangs[numtriags][2] = z1 + (n-1)*dz12 + (m-1)*dz23;
length = sqrt((double) all_triangs[numtriags][0]*all_triangs[numtriags][0]+
all_triangs[numtriags][1]*all_triangs[numtriags][1]+
all_triangs[numtriags][2]*all_triangs[numtriags][2]);
all_triangs[numtriags][0] /= length;
all_triangs[numtriags][1] /= length;
all_triangs[numtriags][2] /= length;
numtriags++;
all_triangs[numtriags][0] = x1 + n*dx12 + (m-1)*dx23;
all_triangs[numtriags][1] = y1 + n*dy12 + (m-1)*dy23;
all_triangs[numtriags][2] = z1 + n*dz12 + (m-1)*dz23;
length = sqrt((double) all_triangs[numtriags][0]*all_triangs[numtriags][0]+
all_triangs[numtriags][1]*all_triangs[numtriags][1]+
all_triangs[numtriags][2]*all_triangs[numtriags][2]);
all_triangs[numtriags][0] /= length;
all_triangs[numtriags][1] /= length;
all_triangs[numtriags][2] /= length;
numtriags++;
if ( m != n )
{
// Draw lower left triangle
all_triangs[numtriags][0] = x1 + n*dx12 + m*dx23;
all_triangs[numtriags][1] = y1 + n*dy12 + m*dy23;
all_triangs[numtriags][2] = z1 + n*dz12 + m*dz23;
length = sqrt((double) all_triangs[numtriags][0]*all_triangs[numtriags][0]+
all_triangs[numtriags][1]*all_triangs[numtriags][1]+
all_triangs[numtriags][2]*all_triangs[numtriags][2]);
all_triangs[numtriags][0] /= length;
all_triangs[numtriags][1] /= length;
all_triangs[numtriags][2] /= length;
numtriags++;
all_triangs[numtriags][0] = x1 + (n-1)*dx12 + m*dx23;
all_triangs[numtriags][1] = y1 + (n-1)*dy12 + m*dy23;
all_triangs[numtriags][2] = z1 + (n-1)*dz12 + m*dz23;
length = sqrt((double) all_triangs[numtriags][0]*all_triangs[numtriags][0]+
all_triangs[numtriags][1]*all_triangs[numtriags][1]+
all_triangs[numtriags][2]*all_triangs[numtriags][2]);
all_triangs[numtriags][0] /= length;
all_triangs[numtriags][1] /= length;
all_triangs[numtriags][2] /= length;
numtriags++;
all_triangs[numtriags][0] = x1 + (n-1)*dx12 + (m-1)*dx23;
all_triangs[numtriags][1] = y1 + (n-1)*dy12 + (m-1)*dy23;
all_triangs[numtriags][2] = z1 + (n-1)*dz12 + (m-1)*dz23;
length = sqrt((double) all_triangs[numtriags][0]*all_triangs[numtriags][0]+
all_triangs[numtriags][1]*all_triangs[numtriags][1]+
all_triangs[numtriags][2]*all_triangs[numtriags][2]);
all_triangs[numtriags][0] /= length;
all_triangs[numtriags][1] /= length;
all_triangs[numtriags][2] /= length;
numtriags++;
}
}
n++;
} while( n<=level );
}
}
//std::cout<<"before indexing of triangs"<<std::endl;
// indexing of triangs
if (level == 1)
{
memcpy(triangs, triang, 20*3*sizeof(int));
numtriags = 20;
}
else
{
//find for every point in triangle list the corresponding index in all_vert
// initialize
for (i=0; i < numtriags; i ++) {
triangs[i] = -1;
}
// find indexes
for(i=0; i<n_vert; i++)
{
for (int j = 0; j < numtriags; j++)
{
if (triangs[j] < 0)
{
if ( (fabs(all_vert[i][0] - all_triangs[j][0]) < epsilon) &&
(fabs(all_vert[i][1] - all_triangs[j][1]) < epsilon) &&
(fabs(all_vert[i][2] - all_triangs[j][2]) < epsilon ) )
{
triangs[j] = i;
}
}
}
}
//for(i=0; i<n_vert; i++)
// std::cout<<triangs[3*i]<<","<<triangs[3*i+1]<<","<<triangs[3*i+2]<<std::endl;
for (i=0; i < numtriags; i ++)
{
if (triangs[i] == -1)
std::cerr << " - " << i << " :" << all_triangs[i][0]
<< "," << all_triangs[i][1] << "," << all_triangs[i][2] << std::endl;
}
// numtriags is the number of vertices in triangles -> divide it by 3
numtriags = numtriags / 3;
}
vtkSmartPointer<vtkIdList> ids = vtkSmartPointer<vtkIdList>::New();
vtkSmartPointer<vtkPoints> pts = vtkSmartPointer<vtkPoints>::New();
vtkPolyData* polyData = vtkPolyData::New();
polyData ->SetPoints (pts);
ids -> SetNumberOfIds(0);
pts -> SetNumberOfPoints(0);
polyData->Allocate();
for (int k = 0; k < n_vert; k++)
{
vtkIdType id;
id = pts->InsertNextPoint(all_vert[k][0],
all_vert[k][1], all_vert[k][2]);
ids->InsertNextId(id);
}
for (int k = 0; k < numtriags; k++)
{
vtkSmartPointer<vtkIdList> tids = vtkSmartPointer<vtkIdList>::New();
tids->SetNumberOfIds(0);
tids->InsertNextId(triangs[3*k]);
tids->InsertNextId(triangs[3*k+1]);
tids->InsertNextId(triangs[3*k+2]);
polyData->InsertNextCell(VTK_TRIANGLE, tids);
}
delete [] all_vert;
delete [] all_triangs;
delete [] triangs;
return polyData;
}
int main( int argc, char *argv[] )
{
PARSE_ARGS;
ImageReaderType::Pointer imageReader = ImageReaderType::New();
ImageType::Pointer image0;
typedef itk::GDCMImageIO ImageIOType;
typedef itk::GDCMSeriesFileNames SeriesFileNames;
typedef itk::ImageSeriesReader< ImageType > SeriesReaderType;
std::string subjectname;
// Read image
if (itksys::SystemTools::FileIsDirectory(inputVolume.c_str() )) // dicom series input
{
std::vector<std::string> lines;
itksys::SystemTools::Split(inputVolume.c_str(), lines, '/');
subjectname = lines[lines.size()-1];
ImageIOType::Pointer gdcmIO = ImageIOType::New();
SeriesFileNames::Pointer it = SeriesFileNames::New();
it->SetInputDirectory( inputVolume.c_str() );
SeriesReaderType::Pointer sReader = SeriesReaderType::New();
const SeriesReaderType::FileNamesContainer & filenames =
it->GetInputFileNames();
sReader->SetFileNames( filenames );
sReader->SetImageIO( gdcmIO );
try
{
sReader->Update();
image0 = sReader->GetOutput();
}
catch (itk::ExceptionObject &excp)
{
std::cerr << "Exception thrown while reading the image" <<
std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
}
else // input is a file
{
itk::GDCMImageIO::Pointer dicomio = itk::GDCMImageIO::New();
if ( dicomio->CanReadFile(inputVolume.c_str()) ) // input is a single dicom file
{
std::string dicompathname = itksys::SystemTools::GetFilenamePath(inputVolume);
std::vector<std::string> lines;
itksys::SystemTools::Split(dicompathname.c_str(), lines, '/');
subjectname = lines[lines.size()-1];
ImageIOType::Pointer gdcmIO = ImageIOType::New();
SeriesFileNames::Pointer it = SeriesFileNames::New();
it->SetInputDirectory( dicompathname.c_str() );
SeriesReaderType::Pointer sReader = SeriesReaderType::New();
const SeriesReaderType::FileNamesContainer & filenames =
it->GetInputFileNames();
sReader->SetFileNames( filenames );
sReader->SetImageIO( gdcmIO );
try
{
sReader->Update();
image0 = sReader->GetOutput();
}
catch (itk::ExceptionObject &excp)
{
std::cerr << "Exception thrown while reading the image" <<
std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
}
else
{
subjectname = itksys::SystemTools::GetFilenameWithoutExtension(inputVolume);
ImageReaderType::Pointer reader2 = ImageReaderType::New();
reader2->SetFileName( inputVolume.c_str() );
try
{
reader2->Update();
image0 = reader2->GetOutput();
}
catch (itk::ExceptionObject &ex)
{
std::cout << ex << std::endl;
return EXIT_FAILURE;
}
}
}
std::cout << "Input image orientation: " << image0->GetDirection() << std::endl;
// convert image into RAS orientation
ImageType::SpacingType spacing = image0->GetSpacing();
float minSpace = spacing[0];
minSpace = minSpace > spacing[1] ? spacing[0] : minSpace;
minSpace = minSpace > spacing[2] ? spacing[0] : minSpace;
spacing.Fill( minSpace );
spacing[2] *= 1.5;
// figure out extent of the volume in the physical space
float xmax = itk::NumericTraits<float>::min();
float ymax = itk::NumericTraits<float>::min();
float zmax = itk::NumericTraits<float>::min();
float xmin = itk::NumericTraits<float>::max();
float ymin = itk::NumericTraits<float>::max();
float zmin = itk::NumericTraits<float>::max();
ImageType::IndexType startIndex = image0->GetLargestPossibleRegion().GetIndex();
ImageType::SizeType size = image0->GetLargestPossibleRegion().GetSize();
ImageType::RegionType region;
ImageType::Pointer dummyImage = ImageType::New();
region.SetIndex(0, 0);
region.SetIndex(1, 0);
region.SetIndex(2, 0);
region.SetSize(0, 2);
region.SetSize(1, 2);
region.SetSize(2, 2);
dummyImage->SetRegions( region );
dummyImage->Allocate();
itk::ImageRegionIteratorWithIndex<ImageType> itd( dummyImage, region );
for (itd.GoToBegin(); !itd.IsAtEnd(); ++itd )
{
ImageType::IndexType idx = itd.GetIndex();
std::cout << idx << " ";
ImageType::PointType pt;
for (int k = 0; k < 3; k++)
{
idx[k] = idx[k]*size[k]+startIndex[k];
}
std::cout << idx << " ";
image0->TransformIndexToPhysicalPoint( idx, pt );
std::cout << pt << std::endl;
if (pt[0] < xmin)
{
xmin = pt[0];
}
if (pt[0] > xmax)
{
xmax = pt[0];
}
if (pt[1] < ymin)
{
ymin = pt[1];
}
if (pt[1] > ymax)
{
ymax = pt[1];
}
if (pt[2] < zmin)
{
zmin = pt[2];
}
if (pt[2] > zmax)
{
zmax = pt[2];
}
}
std::cout << "Physical extent:\n";
std::cout << "[ "
<< xmin << ", " << ymin << ", " << zmin
<< "] -- [ "
<< xmax << ", " << ymax << ", " << zmax
<< "]\n";
ImageType::PointType origin;
origin[0] = xmin; origin[1] = ymin; origin[2] = zmin;
region.SetIndex(0, 0);
region.SetIndex(1, 0);
region.SetIndex(2, 0);
region.SetSize(0, static_cast<int>((xmax-xmin)/spacing[0]));
region.SetSize(1, static_cast<int>((ymax-ymin)/spacing[1]));
region.SetSize(2, static_cast<int>((zmax-zmin)/spacing[2]));
ImageType::Pointer outImage = ImageType::New();
outImage->SetRegions( region );
outImage->SetSpacing( spacing );
outImage->SetOrigin( origin );
outImage->Allocate();
outImage->FillBuffer( 0 );
itk::LinearInterpolateImageFunction< ImageType, double >::Pointer interpolator =
itk::LinearInterpolateImageFunction< ImageType, double >::New();
interpolator->SetInputImage( image0 );
itk::ImageRegionIteratorWithIndex<ImageType> itOut( outImage, region );
for (itOut.GoToBegin(); !itOut.IsAtEnd(); ++itOut)
{
ImageType::IndexType idx = itOut.GetIndex();
ImageType::PointType pt;
outImage->TransformIndexToPhysicalPoint( idx, pt );
itk::ContinuousIndex<double, 3> cIdx;
image0->TransformPhysicalPointToContinuousIndex( pt, cIdx );
if( image0->GetLargestPossibleRegion().IsInside(cIdx) )
{
ImageType::PixelType p = static_cast<ImageType::PixelType>( interpolator->Evaluate(pt) );
itOut.Set( p );
}
}
// figure out the top of the head
int nTopSlice = FindTopSlice( outImage );
int nStartSlice = nTopSlice - static_cast<int>(150.0/spacing[2]);
int numberOfSlices = nTopSlice-nStartSlice +1;
if (nStartSlice < region.GetIndex(2))
{
nStartSlice = region.GetIndex(2);
numberOfSlices = nTopSlice-nStartSlice+1;
}
region.SetIndex(2, nStartSlice);
region.SetSize(2, numberOfSlices);
std::cout << "Extract region: " << region << std::endl;
itk::ExtractImageFilter<ImageType, ImageType>::Pointer extract = itk::ExtractImageFilter<ImageType, ImageType>::New();
extract->SetInput( outImage );
extract->SetExtractionRegion( region );
extract->Update();
typedef itk::BinaryBallStructuringElement<double, 3> KernelType;
typedef itk::GrayscaleFunctionErodeImageFilter< ImageType, ImageType, KernelType> GrayScaleOpeningFilterType;
// typedef itk::GrayscaleMorphologicalOpeningImageFilter< ImageType, ImageType, KernelType> GrayScaleOpeningFilterType;
GrayScaleOpeningFilterType::Pointer grayopening = GrayScaleOpeningFilterType::New();
grayopening->SetInput( outImage );
// Create the structuring element
KernelType ball0;
KernelType::SizeType ballSize0;